Incidental Mutation 'R5484:Alx1'
ID 430321
Institutional Source Beutler Lab
Gene Symbol Alx1
Ensembl Gene ENSMUSG00000036602
Gene Name ALX homeobox 1
Synonyms Cart1
MMRRC Submission 043045-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5484 (G1)
Quality Score 225
Status Validated
Chromosome 10
Chromosomal Location 102843708-102865501 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 102861177 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Valine at position 117 (D117V)
Ref Sequence ENSEMBL: ENSMUSP00000152018 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000040859] [ENSMUST00000167156] [ENSMUST00000217946] [ENSMUST00000218282] [ENSMUST00000219194] [ENSMUST00000218681]
AlphaFold Q8C8B0
Predicted Effect probably damaging
Transcript: ENSMUST00000040859
AA Change: D117V

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000042512
Gene: ENSMUSG00000036602
AA Change: D117V

DomainStartEndE-ValueType
HOX 132 194 1.84e-25 SMART
Pfam:OAR 301 321 7.3e-13 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000164226
Predicted Effect probably damaging
Transcript: ENSMUST00000167156
AA Change: D117V

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000129230
Gene: ENSMUSG00000036602
AA Change: D117V

DomainStartEndE-ValueType
HOX 132 194 1.84e-25 SMART
Pfam:OAR 302 320 2.3e-12 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000170026
Predicted Effect possibly damaging
Transcript: ENSMUST00000217946
AA Change: D117V

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)
Predicted Effect probably damaging
Transcript: ENSMUST00000218282
AA Change: D117V

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
Predicted Effect probably damaging
Transcript: ENSMUST00000219194
AA Change: D117V

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
Predicted Effect probably damaging
Transcript: ENSMUST00000218681
AA Change: D117V

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218508
Meta Mutation Damage Score 0.1528 question?
Coding Region Coverage
  • 1x: 98.3%
  • 3x: 97.3%
  • 10x: 95.3%
  • 20x: 91.4%
Validation Efficiency 97% (76/78)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The specific function of this gene has yet to be determined in humans; however, in rodents, it is necessary for survival of the forebrain mesenchyme and may also be involved in development of the cervix. Mutations in the mouse gene lead to neural tube defects such as acrania and meroanencephaly. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutant mice exhibit perinatal lethality with acrania and meroanencephaly, but the neural tube closure defect can be ameliorated with prenatal folic acid treatment. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921509C19Rik T C 2: 151,313,851 (GRCm39) H609R probably benign Het
Abca6 A T 11: 110,074,899 (GRCm39) V1388E probably damaging Het
Ascl4 T C 10: 85,764,401 (GRCm39) L16P probably damaging Het
Atp4a G A 7: 30,420,097 (GRCm39) probably benign Het
Btnl10 G A 11: 58,814,651 (GRCm39) V444M probably damaging Het
Camkv A T 9: 107,823,345 (GRCm39) N124Y probably damaging Het
Catsperb T C 12: 101,542,175 (GRCm39) L625P probably benign Het
Ccdc171 A G 4: 83,612,199 (GRCm39) I973V probably benign Het
Celsr1 T C 15: 85,815,483 (GRCm39) D1844G probably benign Het
Chd7 G C 4: 8,828,258 (GRCm39) K1066N probably damaging Het
Cmklr1 C G 5: 113,752,990 (GRCm39) D4H possibly damaging Het
Corin T C 5: 72,515,827 (GRCm39) D409G probably benign Het
Cry1 T C 10: 84,982,588 (GRCm39) probably null Het
Cttnbp2 T A 6: 18,427,689 (GRCm39) probably benign Het
Cyrib T A 15: 63,815,056 (GRCm39) T139S probably damaging Het
Dmxl1 T A 18: 50,022,531 (GRCm39) V1623E probably damaging Het
Dnah6 G T 6: 73,069,099 (GRCm39) D2477E possibly damaging Het
Dnajb12 GC G 10: 59,728,574 (GRCm39) probably null Het
Dop1a C G 9: 86,427,341 (GRCm39) R2164G probably damaging Het
Dsp A G 13: 38,368,014 (GRCm39) T678A possibly damaging Het
Farsb A C 1: 78,452,833 (GRCm39) I51S probably damaging Het
Gm10220 T A 5: 26,322,930 (GRCm39) I161L possibly damaging Het
Gm10782 G T 13: 56,510,987 (GRCm39) noncoding transcript Het
Gm12830 A T 4: 114,702,248 (GRCm39) T137S unknown Het
Gopc A G 10: 52,234,942 (GRCm39) L67P probably damaging Het
Hmcn1 T C 1: 150,551,291 (GRCm39) I2655V probably benign Het
Hmcn2 C T 2: 31,283,066 (GRCm39) Q1981* probably null Het
Ifi209 T A 1: 173,468,640 (GRCm39) S157T probably benign Het
Ift56 T G 6: 38,366,057 (GRCm39) C124W probably benign Het
Iqcf1 A T 9: 106,379,107 (GRCm39) I74F probably damaging Het
Irf3 A T 7: 44,649,382 (GRCm39) R78W probably damaging Het
Kank4 T C 4: 98,663,022 (GRCm39) D722G probably benign Het
Loxl1 A G 9: 58,198,065 (GRCm39) V597A possibly damaging Het
Marveld1 T C 19: 42,136,272 (GRCm39) L62P probably damaging Het
Mga T G 2: 119,747,107 (GRCm39) D419E possibly damaging Het
Mroh2a A G 1: 88,186,386 (GRCm39) S64G probably benign Het
Mroh2b A G 15: 4,938,463 (GRCm39) K251E possibly damaging Het
Myh4 A G 11: 67,142,644 (GRCm39) E935G probably damaging Het
Nat8f2 C A 6: 85,844,994 (GRCm39) A123S possibly damaging Het
Niban1 A G 1: 151,593,837 (GRCm39) T841A probably benign Het
Or4d11 G A 19: 12,013,192 (GRCm39) L305F probably benign Het
Pcdha9 T A 18: 37,131,156 (GRCm39) V75E probably damaging Het
Pebp4 A T 14: 70,200,991 (GRCm39) probably null Het
Pitx1 A G 13: 55,974,166 (GRCm39) S222P probably benign Het
Plekhg3 G A 12: 76,625,174 (GRCm39) V1339M possibly damaging Het
Plekhs1 C T 19: 56,468,260 (GRCm39) S276L possibly damaging Het
Plin4 T C 17: 56,411,932 (GRCm39) T700A possibly damaging Het
Plxnb2 T C 15: 89,048,412 (GRCm39) probably null Het
Pms2 T C 5: 143,864,943 (GRCm39) I675T probably damaging Het
Polrmt A G 10: 79,577,888 (GRCm39) L268P probably damaging Het
Rtp1 A G 16: 23,248,025 (GRCm39) T33A probably benign Het
Safb2 T C 17: 56,882,346 (GRCm39) probably benign Het
Sdk1 C A 5: 142,085,941 (GRCm39) P1383Q probably damaging Het
Setdb1 A T 3: 95,244,569 (GRCm39) C758S probably damaging Het
Sh3gl2 T C 4: 85,317,160 (GRCm39) probably benign Het
Slc13a2 G A 11: 78,295,648 (GRCm39) probably benign Het
Slc35b1 T C 11: 95,278,631 (GRCm39) Y126H probably damaging Het
Strip2 C A 6: 29,917,154 (GRCm39) probably benign Het
Tbx4 A G 11: 85,805,230 (GRCm39) T440A probably damaging Het
Tcf7l2 C A 19: 55,907,940 (GRCm39) probably null Het
Tgfb1 A C 7: 25,387,574 (GRCm39) D94A probably benign Het
Tmem132b T C 5: 125,864,797 (GRCm39) C968R probably damaging Het
Tmem176b T A 6: 48,811,467 (GRCm39) M61L probably benign Het
Tmem258 A G 19: 10,184,689 (GRCm39) probably null Het
Tpr T C 1: 150,302,639 (GRCm39) L1379S probably benign Het
Vmn2r44 T C 7: 8,383,123 (GRCm39) D157G possibly damaging Het
Wfdc8 T C 2: 164,439,649 (GRCm39) I244M probably benign Het
Zfp341 T C 2: 154,466,921 (GRCm39) S97P probably benign Het
Zfp655 T C 5: 145,180,445 (GRCm39) V101A probably benign Het
Zfp788 T C 7: 41,299,277 (GRCm39) S586P probably damaging Het
Zfp874b C T 13: 67,629,373 (GRCm39) V52I possibly damaging Het
Other mutations in Alx1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02331:Alx1 APN 10 102,858,160 (GRCm39) missense possibly damaging 0.93
IGL02508:Alx1 APN 10 102,858,054 (GRCm39) missense probably damaging 0.99
IGL03079:Alx1 APN 10 102,845,209 (GRCm39) missense probably damaging 1.00
R1345:Alx1 UTSW 10 102,864,353 (GRCm39) missense possibly damaging 0.86
R1370:Alx1 UTSW 10 102,864,353 (GRCm39) missense possibly damaging 0.86
R1846:Alx1 UTSW 10 102,861,165 (GRCm39) missense possibly damaging 0.88
R1912:Alx1 UTSW 10 102,861,222 (GRCm39) missense probably damaging 1.00
R4649:Alx1 UTSW 10 102,845,193 (GRCm39) missense probably damaging 0.99
R4767:Alx1 UTSW 10 102,861,047 (GRCm39) nonsense probably null
R5979:Alx1 UTSW 10 102,858,120 (GRCm39) missense probably damaging 1.00
R6115:Alx1 UTSW 10 102,864,304 (GRCm39) missense possibly damaging 0.78
R6919:Alx1 UTSW 10 102,861,061 (GRCm39) missense probably damaging 1.00
R7781:Alx1 UTSW 10 102,845,053 (GRCm39) missense probably damaging 0.99
R8166:Alx1 UTSW 10 102,845,224 (GRCm39) missense probably damaging 1.00
R8238:Alx1 UTSW 10 102,858,076 (GRCm39) missense possibly damaging 0.80
R8275:Alx1 UTSW 10 102,864,250 (GRCm39) missense probably benign 0.04
R9219:Alx1 UTSW 10 102,858,121 (GRCm39) missense probably damaging 0.98
R9323:Alx1 UTSW 10 102,858,124 (GRCm39) nonsense probably null
R9482:Alx1 UTSW 10 102,864,335 (GRCm39) missense probably benign
R9654:Alx1 UTSW 10 102,858,093 (GRCm39) missense probably benign 0.02
Predicted Primers PCR Primer
(F):5'- GTCTTAGCTGAGAATGCTTCTTCC -3'
(R):5'- GTATGTTTCACCACCCTGAGTATC -3'

Sequencing Primer
(F):5'- GAAAAGCCCTGCCTTTTGG -3'
(R):5'- ACCCTGAGTATCGCTGTTTTC -3'
Posted On 2016-10-05